If this is the first time that something like this has ever happened I am shocked that they would be doing this. If they take to to court you can show the judge your previous payment history with the landlord and try the excuse "it was an honest mistake.''
Now if they are really going to go through with this, unfortunately the responsibility is on you to prove they lost the check, I would say that they, unfortunately, have a legal right to issue the charges, so you might have to pay and then move out!!!!!!!!!!!!
I know it's not what you wanted to hear, but it may boil down to this. Sorry to hear about this.